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This Week in Nature: Mar 3, 2011

In a paper published online in advance in Nature this week, investigators at the Centre for Lymphoid Cancers and the Centre for Translational and Applied Genomics in Vancouver report their use of RNA-seq to show that a gene fusion involving the major histocompatibility complex class II transactivator CIITA occurs frequently in lymphoid cancers. The team found that "CIITA breaks are highly recurrent in primary mediastinal B-cell lymphoma and classical Hodgkin lymphoma," and that alterations of this gene "impact survival in primary mediastinal B-cell lymphoma."

In another Nature advance online publication, researchers in Sweden and Japan show that "chromosome length influences replication-induced topological stress" in S. cerevisiae. In its experimental manipulations, the team found that cells expressing mutated versions of the cohesion- and condensin-related Smc5/6 complex show "late replication delay of longer, but not shorter, chromosomes." As a result of its analysis, the team suggests that the "Smc5/6 complex facilitates fork rotation by sequestering nascent chromatid intertwinings that form behind the replication machinery."

An international research team led by investigators at Thomas Jefferson University in Philadelphia shows that FADD and RIP1 engage in a cell-type specific interplay that is "critical for the regulation of apoptosis and necrosis during embryogenesis and lymphocyte function." In Fadd knockout mice, the team found that "RIP1 deficiency allowed normal embryogenesis." However, the team found that "the developmental defect of Rip1−/− lymphocytes was partially corrected by FADD deletion." And in Fadd−/−Rip1−/− double-knockout mouse models, the team shows that "T cells are resistant to death induced by Fas or TNF-α and show reduced NF-κB activity."

In a trio of papers appearing online in advance in Nature Genetics this week, two international teams report on mutations in five pre-replication complex genes — ORC1, ORC4, ORC6, CDT1 and CDC6 — that cause Meier-Gorlin syndrome and show that "mutations in ORC1, encoding the largest subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome." A third team reports its use of "marker-assisted mapping in multiple families from a founder population and traditional coding exon sequencing of positional candidate genes" to identify ORC4 missense mutations in affected individuals.

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.